WDR3 RNA-Seq in K562

General Information


RBP	WDR3
Cell_Line	K562
Method	shRNA
Exp_Name	WDR3-BGKLV34-K562
ENCODE_series_ID	ENCSR850PEM
Batch_ID	BGKLV34
Pool ID	Pool-160912
Local_Set_Name	set34
ENCODE_KD_Exp_ID	ENCSR334BTA
ENCODE_CN_Exp_ID	ENCSR174OYC
Rep1	WDR3_BGKLV34-49
Rep2	WDR3_BGKLV34-50
CN1	NT_BGKLV34-1
CN2	NT_BGKLV34-2
Rep1_qPCR	83.8
Rep2_qPCR	81.7
Rep1_WB	94.4
Rep2_WB	95.1
Antibody Cat#	A301-553A
Antibody Lot#	A301-553A
Antibody DCC ID	ENCAB768ADR
Status	Released
Project	ENCODE3
ID	728

Experiment Information (Status: Released)

	BGKLV34-49	BGKLV34-50
idx	712	713
TRCN#_or_BGC#	TRCN0000146609	TRCN0000146609
shRNA_or_gRNA_sequence	CCTGGAATACAAGATACTCTT	CCTGGAATACAAGATACTCTT
PAM
Name	WDR3	WDR3
Sample_ID	BGKLV34-49	BGKLV34-50
transduction_Date	11/4/2015	11/4/2015
days
RBP_name	WDR3	WDR3
qPCR_result	83.8	81.7
Ave_qPCR	82.8
RT-qPCR_primer-F	tcagctaggaggcagactgg
RT-qPCR_primer-R	gtgcccctttagacggtaca
protein_conc	4521	3782
WB_result	94.4	95.1
Ave_WB	94.7
WB_DONE_date	2/22/2016
MW	106kDa	WES
IP	1	1
antibody_Cat#	A301-553A	A301-553A
Antibody DCC ID	ENCAB768ADR	ENCAB768ADR
submitted_to_DCC_date	3/8/2016
Rep1_TPM	29.5747421	0
Rep2_TPM	11.8098055	0
Action
Library_start_date	3/9/2016	3/9/2016
repeat_library
Note
ID	801	802

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
WDR3	Product_ID: A301-553A Lot_ID: 1 Source: Bethyl Labs Target Name: WDR3-human

Experiment Status

	BGKLV34-49	BGKLV34-50
Sample_ID	BGKLV34-49	BGKLV34-50
Sample Name	WDR3_BGKLV34-49	WDR3_BGKLV34-50
Sample Name	WDR3_BGKLV34-49	WDR3_BGKLV34-50
RBP	WDR3	WDR3
Cell_Line	K562	K562
Exp UID
Status	Released	Released
Status_date	2016-09-24	2016-09-24
Project	ENCODE3	ENCODE3
Note
ID	1245	1246

Library-Prep
Sequencing

Library-Prep Information

	BGKLV34-49	BGKLV34-50
Sample #
Sample Name	WDR3-BGKLV34-49	WDR3-BGKLV34-50
Sample_Name_Alias	WDR3_BGKLV34-49	WDR3_BGKLV34-50
Index Well Position	S13	S14
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2016-03-09	2016-03-09
Lib_ID	Lib-160309	Lib-160309
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV33-34-25B-32/set1/E4.png	DNA_Library_LV33-34-25B-32/set1/F4.png
RIN	10.0	10.0
libSample_RNA_Well	RNA_Library_LV32-33-34/set1/C6.png	RNA_Library_LV32-33-34/set1/D6.png
SampleQC_method
SampleQC_date
Sample_ID	BGKLV34-49	BGKLV34-50
RBP	WDR3	WDR3
Batch_ID	BGKLV34	BGKLV34
WB_result	94.400	95.100
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2930	2931

Sequencing Information

	BGKLV34-49	BGKLV34-50
Sample_ID	BGKLV34-49	BGKLV34-50
Sample Name	WDR3_BGKLV34-49	WDR3_BGKLV34-50
Pool ID	Pool-160912	Pool-160912
LocalServer_folder	set34	set34
total_reads	68,321,710	70,117,438
total_aligned_reads	58,768,242	60,675,434
unique_aligned_reads	53,755,072	55,326,638
percent_uniqueAligned	0.78679	0.78906
correlation_replicates	0.997114	0.997114
spikein_reads	196,136	227,200
percent_spikeins	0.00287	0.00324
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1579	1580

Data Submission Information

	BGKLV34-49	BGKLV34-49
ENCODE_alias	brenton-graveley:WDR3_BGKLV34	brenton-graveley:WDR3-BGKLV34-K562
ENCODE_accession	ENCSR334BTA	ENCSR850PEM
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGKLV34-49	BGKLV34-49
Sample Name	WDR3_BGKLV34-49	WDR3_BGKLV34-49
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-09-23	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3162	7038

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
WDR3_BGKLV34-49_AGTCAA_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1579	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21538
WDR3_BGKLV34-49_AGTCAA_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1579	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21558
WDR3_BGKLV34-49_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1579					GRCh38	V40	WDR3_BGKLV34-49_AGTCAA_L004_001.R1.fastq.gz,WDR3_BGKLV34-49_AGTCAA_L004_001.R2.fastq.gz		ENCORE2	21578
WDR3_BGKLV34-49_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1579					GRCh38	V40	WDR3_BGKLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	21598
WDR3_BGKLV34-49_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1579					GRCh38	V40	WDR3_BGKLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	21618
WDR3_BGKLV34-49_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1579					GRCh38	V40	WDR3_BGKLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	21638
WDR3_BGKLV34-49_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1579					GRCh38	V40	WDR3_BGKLV34-49/Aligned.sortedByCoord.out.bam		ENCORE2	21658
WDR3_BGKLV34-49_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1579					GRCh38	V40	WDR3_BGKLV34-49_AGTCAA_L004_001.R1.fastq.gz,WDR3_BGKLV34-49_AGTCAA_L004_001.R2.fastq.gz		ENCORE2	21678
WDR3_BGKLV34-50_AGTTCC_L004_001.R1.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1580	HiSeq2500	100	paired-ended	1				NT_BGKLV34-1_CGTACG_L002_001.R1.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R1.fastq.gz	ENCODE3	21539
WDR3_BGKLV34-50_AGTTCC_L004_001.R2.fastq.gz	ENCODE_DATA/set34/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1580	HiSeq2500	100	paired-ended	2				NT_BGKLV34-1_CGTACG_L002_001.R2.fastq.gz,NT_BGKLV34-2_GAGTGG_L002_001.R2.fastq.gz	ENCODE3	21559
WDR3_BGKLV34-50_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1580					GRCh38	V40	WDR3_BGKLV34-50_AGTTCC_L004_001.R1.fastq.gz,WDR3_BGKLV34-50_AGTTCC_L004_001.R2.fastq.gz		ENCORE2	21579
WDR3_BGKLV34-50_Signal.Unique.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1580					GRCh38	V40	WDR3_BGKLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	21599
WDR3_BGKLV34-50_Signal.Unique.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1580					GRCh38	V40	WDR3_BGKLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	21619
WDR3_BGKLV34-50_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1580					GRCh38	V40	WDR3_BGKLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	21639
WDR3_BGKLV34-50_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set34/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1580					GRCh38	V40	WDR3_BGKLV34-50/Aligned.sortedByCoord.out.bam		ENCORE2	21659
WDR3_BGKLV34-50_quant.sf	ENCODE_DATA/set34/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1580					GRCh38	V40	WDR3_BGKLV34-50_AGTTCC_L004_001.R1.fastq.gz,WDR3_BGKLV34-50_AGTTCC_L004_001.R2.fastq.gz		ENCORE2	21679